Interpretive Summary: Theobroma cacao, the source of cocoa beans for chocolate, is an important tropical agriculture commodity that is affected by a number of fungal pathogens and insect pests, as well as concerns about yield and quality. We are trying to find molecular genetic markers that are linked to disease resistance and other important economic traits to aid in a marker assisted selection (MAS) breeding program for cacao to ensure a reliable supply of cocoa for the US confectionary industry. The drastic reductions in cost and time associated with the collection of DNA sequence and genotype data have revolutionized genetic mapping in model systems (e.g. humans, Arabidopsis) and also promise to significantly enhance the power and resolution of genetic mapping in agricultural systems. Progress in this domain depends crucially on the adoption of rapid and cost-effective genotyping assays that exploit the high-throughput power of next-generation DNA sequencing. Here we report preliminary results of a novel Genotyping-By-Sequencing (GBS) approach applied to an F1 mapping population of cacao (Theobroma cacao). We present summaries of the SNP map generated from whole-genome sequences from the two parents of the population and provide preliminary results from GBS applied to 40 F1 offspring using Illumina GAII sequencing. GBS has the potential to replace genotyping microarrays as a more cost-effective and high-throughput method for mid-density (10k – 100k SNPs) genotyping of mapping populations to identify molecular markers associated with disease resistance and other important horticultural traits. Our results are important to scientists trying to understand the mechanism of disease resistance and, eventually, to cacao farmers who will benefit from superior disease resistant and more productive cultivars produced through our MAS breeding program.

Technical Abstract:
The drastic reductions in cost and time associated with the collection of DNA sequence and genotype data have revolutionized genetic mapping in model systems (e.g. humans, Arabidopsis) and also promise to significantly enhance the power and resolution of genetic mapping in agricultural systems. Progress in this domain depends crucially on the adoption of rapid and cost-effective genotyping assays that exploit the high-throughput power of next-generation DNA sequencing. Here we report preliminary results of a novel Genotyping-By-Sequencing (GBS) approach applied to an F1 mapping population of cacao (Theobroma cacao). We present summaries of the SNP map generated from whole-genome sequences from the two parents of the population and provide preliminary results from GBS applied to 40 F1 offspring using Illumina GAII sequencing. GBS has the potential to replace genotyping microarrays as a more cost-effective and high-throughput method for mid-density (10k – 100k SNPs) genotyping of mapping populations. This is of particular importance for tropical crops such as cacao, for which the microarray technology may result unaffordable in research institutes from developing countries. However, we discuss several challenges associated with the use of GBS in heterozygous systems (e.g. calling heterozygotes, phasing, imputation) that must first be overcome before it is adopted on a wider scale